ihw.DESeqResults {IHW} | R Documentation

## ihw.DESeqResults: IHW method dispatching on DESeqResults objects

### Description

ihw.DESeqResults: IHW method dispatching on DESeqResults objects

### Usage

    ## S3 method for class 'DESeqResults'
    ihw(deseq_res, filter = "baseMean", alpha = 0.1,
      adjustment_type = "BH", ...)

### Arguments

`deseq_res` | "DESeqResults" object
`filter` | Vector of length equal to number of rows of deseq_res object. This is used for the covariates in the call to ihw. Can also be a character, in which case deseq_res[[filter]] is used as the covariate
`alpha` | Numeric, sets the nominal level for FDR control.
`adjustment_type` | Character ("BH" or "bonferroni") depending on whether you want to control FDR or FWER.
`...` | Other optional keyword arguments passed to ihw.

### Value

A "DESeqResults" object, which includes weights and adjusted p-values returned by IHW. In addition, includes a metadata slot with an "ihwResult" object.

### See Also

ihw, ihwResult

### Examples

    ## Not run:
       library("DESeq2")
       library("airway")
       data("airway")
       dds <- DESeqDataSet(se = airway, design = ~ cell + dex)
       dds <- DESeq(dds)
       deseq_res <- results(dds)
       deseq_res <- ihw(deseq_res, alpha=0.1)
       #equivalent: deseq_res2 <- results(dds, filterFun = ihw)

    ## End(Not run)

[Package IHW version 1.12.0 Index]